Mark DePristo 251983b8fb Add GATK-wide command line argument to control the maximum runtime allowed for the GATK ... -- Providing this optional argument -maxRuntime (in -maxRuntimeUnits units) causes the GATK to exit gracefully when the max. runtime has been exceeded. By cleanly I mean that the engine simply stops at the next available cycle in the walker as through the end of processing had been reached. This means that all output files are closed properly, etc. -- Emits an info message that looks like "INFO 10:36:52,723 MicroScheduler - Aborting execution (cleanly) because the runtime has exceeded the requested maximum 10.0000 s". Otherwise there's currently no way to differentiate a truly completed run from a timelimit exceeded run, which may be a useful thing for a future update -- Resolves GSA-630 / GATK max runtime to deal with bad LSA calling? -- Added new JIRA entry for Ami to restart chr1 macarthur with this argument set to -maxRuntime 1 -maxRuntimeUnits DAYS to see if we can do all of chr1 in one weekend.		2012-10-26 13:18:34 -04:00
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DbsnpArgumentCollection.java	Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing.	2011-10-27 13:58:19 -04:00
GATKArgumentCollection.java	Add GATK-wide command line argument to control the maximum runtime allowed for the GATK	2012-10-26 13:18:34 -04:00
StandardCallerArgumentCollection.java	The default value for --contamination_fraction_to_filter is now 0.05 (5%) in both UG and HC. Users of GATK-lite get pushed down to 0% by default (since it's not enabled) or get a user error if they try to set it.	2012-10-26 01:04:51 -04:00
StandardVariantContextInputArgumentCollection.java	Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing.	2011-10-27 13:58:19 -04:00
ValidationExclusion.java	BCF2 cleanup	2012-06-26 15:28:33 -04:00